TTˉT\bar{T} deformation of chiral bosons and Chern-Simons AdS3_3 gravity

We study the $T\bar{T}$ deformation of the chiral bosons and show the equivalence between the chiral bosons of opposite chiralities and the scalar fields at the Hamiltonian level under the deformation. We also derive the deformed Lagrangian of more generic theories which contain an arbitrary number of chiral bosons to all orders. By using these results, we derive the $T\bar{T}$ deformed boundary action of the AdS$_3$ gravity theory in the Chern-Simons formulation. We compute the deformed one-loop torus partition function, which satisfies the $T\bar{T}$ flow equation up to the one-loop order. Finally, we calculate the deformed stress tensor of a solution describing a BTZ black hole in the boundary theory, which coincides with the boundary stress tensor derived from the BTZ black hole with a finite cutoff.Comment: 29 pages, references adde

Robust hashing for image authentication using quaternion discrete Fourier transform and log-polar transform

International audienceIn this work, a novel robust image hashing scheme for image authentication is proposed based on the combination of the quaternion discrete Fourier transform (QDFT) with the log-polar transform. QDFT offers a sound way to jointly deal with the three channels of color images. The key features of the present method rely on (i) the computation of a secondary image using a log-polar transform; and (ii) the extraction from this image of low frequency QDFT coefficients' magnitude. The final image hash is generated according to the correlation of these magnitude coefficients and is scrambled by a secret key to enhance the system security. Experiments were conducted in order to analyze and identify the most appropriate parameter values of the proposed method and also to compare its performance to some reference methods in terms of receiver operating characteristics curves. The results show that the proposed scheme offers a good sensitivity to image content alterations and is robust to the common content-preserving operations, and especially to large angle rotation operations

Identification and characterization of pseudogenes in the rice gene complement

<p>Abstract</p> <p>Background</p> <p>The Osa1 Genome Annotation of rice (<it>Oryza sativa </it>L. ssp. <it>japonica </it>cv. Nipponbare) is the product of a semi-automated pipeline that does not explicitly predict pseudogenes. As such, it is likely to mis-annotate pseudogenes as functional genes. A total of 22,033 gene models within the Osa1 Release 5 were investigated as potential pseudogenes as these genes exhibit at least one feature potentially indicative of pseudogenes: lack of transcript support, short coding region, long untranslated region, or, for genes residing within a segmentally duplicated region, lack of a paralog or significantly shorter corresponding paralog.</p> <p>Results</p> <p>A total of 1,439 pseudogenes, identified among genes with pseudogene features, were characterized by similarity to fully-supported gene models and the presence of frameshifts or premature translational stop codons. Significant difference in the length of duplicated genes within segmentally-duplicated regions was the optimal indicator of pseudogenization. Among the 816 pseudogenes for which a probable origin could be determined, 75% originated from gene duplication events while 25% were the result of retrotransposition events. A total of 12% of the pseudogenes were expressed. Finally, F-box proteins, BTB/POZ proteins, terpene synthases, chalcone synthases and cytochrome P450 protein families were found to harbor large numbers of pseudogenes.</p> <p>Conclusion</p> <p>These pseudogenes still have a detectable open reading frame and are thus distinct from pseudogenes detected within intergenic regions which typically lack definable open reading frames. Families containing the highest number of pseudogenes are fast-evolving families involved in ubiquitination and secondary metabolism.</p

Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts

BACKGROUND: The Solanaceae is a family of closely related species with diverse phenotypes that have been exploited for agronomic purposes. Previous studies involving a small number of genes suggested sequence conservation across the Solanaceae. The availability of large collections of Expressed Sequence Tags (ESTs) for the Solanaceae now provides the opportunity to assess sequence conservation and divergence on a genomic scale. RESULTS: All available ESTs and Expressed Transcripts (ETs), 449,224 sequences for six Solanaceae species (potato, tomato, pepper, petunia, tobacco and Nicotiana benthamiana), were clustered and assembled into gene indices. Examination of gene ontologies revealed that the transcripts within the gene indices encode a similar suite of biological processes. Although the ESTs and ETs were derived from a variety of tissues, 55–81% of the sequences had significant similarity at the nucleotide level with sequences among the six species. Putative orthologs could be identified for 28–58% of the sequences. This high degree of sequence conservation was supported by expression profiling using heterologous hybridizations to potato cDNA arrays that showed similar expression patterns in mature leaves for all six solanaceous species. 16–19% of the transcripts within the six Solanaceae gene indices did not have matches among Solanaceae, Arabidopsis, rice or 21 other plant gene indices. CONCLUSION: Results from this genome scale analysis confirmed a high level of sequence conservation at the nucleotide level of the coding sequence among Solanaceae. Additionally, the results indicated that part of the Solanaceae transcriptome is likely to be unique for each species

Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

<p>Abstract</p> <p>Background</p> <p>The Solanaceae family contains a number of important crop species including potato (<it>Solanum tuberosum</it>) which is grown for its underground storage organ known as a tuber. Albeit the 4^thmost important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses.</p> <p>Results</p> <p>In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC) clone library (87 Mb) and sequencing of 22 potato BAC clones (2.9 Mb). The GC content of potato is very similar to <it>Solanum lycopersicon </it>(tomato) and other dicotyledonous species yet distinct from the monocotyledonous grass species, <it>Oryza sativa</it>. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two <it>Solanum </it>species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed.</p> <p>Conclusion</p> <p>Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that this conservation can be leveraged in genomic applications including cross-species annotation and genome sequencing initiatives. While tomato and potato share genic features, they differ in their repetitive sequence content and composition suggesting that repetitive sequences may have a more significant role in shaping speciation than previously reported.</p

A SURVEY OF COLLABORATIVE FILTERING BASED ON NEAREST-NEIGHBORS

This paper explains the k-NN classification algorithm and its operator in RapidMiner. The Use Case of this chapter applies the k-NN operator on the Teacher Evaluation dataset. The operators explained in this chapter are: Read URL, Rename, Numerical to Binominal, Numerical to Polynominal, Set Role, Split Validation, Apply Model, and Performance. The k-Nearest Neighbor algorithm is based on learning by analogy, that is, by comparing a given test example with the training examples that are similar to it. The training examples are described by n attributes. Each example represents a point in an n-dimensional space. In this way, all of the training examples are stored in an n-dimensional pattern space. When given an unknown example, the k-nearest neighbor algorithm searches the pattern space for the k training examples that are closest to the unknown example. These k training examples are the k “nearest neighbors” of the unknown example. The “Closeness” is defined in terms of a distance metric, such as the Euclidean distance